Data Set "Benchmarking of Vibrational Exciton Models Against Quantum-Chemical Localized-Mode Calculations"

This data set accompanies the publication "Benchmarking of Vibrational Exciton Models Against Quantum-Chemical Localized-Mode Calculations" by Anna M. van Bodegraven, Kevin Focke, Mario Wolter, and Christoph R. Jacob (TU Braunschweig, Germany) 

It contains the following files:

Directory 'AIM':

    - input (structure.pdb and *_input.txt) and results (*.log and      Hamiltonian/AtomPos/Dipole/Parameters.txt) from frequency calculations      with the Amide-I-maps (AIM) program for six polypeptide test cases      (1gpB_310, ala_310, ala_hairpin, ala_helix, ala_strand, and trpzip),          each in vacuo or water with three different maps (Jansen, Skinner,       Tokmakoff) for 11 snapshots based on a MD run.    - the used topology files for vacuo calculation are at the top level      for each structure. For the water calculations, they are within the      folder for the respective snapshot.    - to rerun the calculations, you will have to change the paths in       the *_input.txt files (topfile, trjfile, sourcedir) accordingly    Directory 'SNF':

    - results (*.dat, *.out, coord and control) from frequency calculations       using Turbomole, SNF, and LocVib for six polypeptide test cases      (1gpB_310, ala_310, ala_hairpin, ala_helix, ala_strand, and trpzip)       each in vacuo or water for 11 snapshots based on a MD run.      Directory 'Handling_Data':

    - contains all used notebooks to extract the data, plot the figures       and calculate the errors    - to use the notebooks, start with the Dictionary_setup_for_data_for_paper.ipynb       to set up the main dictionary from the calculated data    - the RMSD_Error_vacuo/water.ipynb is used to calculate the overall shifts       and generates a map-dependent mean value to shift the frequencies of AIM    - Frequencies.ipynb and Couplings.ipynb are used to plot the figures     - RMSD_values_vacuo/water.ipynb show the calculations for the statistical analysis